Comments (5)
Could you provide the error log file?
from nextdenovo.
error log:
$cat Pp.sh.e
hostname
- hostname
cd /GPFS/zhangli_lab_permanent/zengpeng/Pp/01_rundir/02.cns_align/01.get_cns.sh.work/get_cns000 - cd /GPFS/zhangli_lab_permanent/zengpeng/Pp/01_rundir/02.cns_align/01.get_cns.sh.work/get_cns000
time python /usr/nzx-cluster/apps/NextDenovo/NextDenovo/lib/nextcorrect.py -f /GPFS/zhangli_lab_permanent/zengpeng/Pp/./01_rundir/02.cns_align//01.get_cns.input.idxs -i /GPFS/zhangli_lab_permanent/zengpeng/Pp/01_rundir/01.raw_align/03.sort_align.sh.work/sort_align000/input.seed.053.sorted.ovl -p 15 -max_lq_length 10000 -o cns.fasta; - python /usr/nzx-cluster/apps/NextDenovo/NextDenovo/lib/nextcorrect.py -f /GPFS/zhangli_lab_permanent/zengpeng/Pp/./01_rundir/02.cns_align//01.get_cns.input.idxs -i /GPFS/zhangli_lab_permanent/zengpeng/Pp/01_rundir/01.raw_align/03.sort_align.sh.work/sort_align000/input.seed.053.sorted.ovl -p 15 -max_lq_length 10000 -o cns.fasta
[INFO] 2019-11-26 10:01:20,051 Corrected step options:
[INFO] 2019-11-26 10:01:20,051 Namespace(blacklist='/GPFS/zhangli_lab_permanent/zengpeng/Pp/01_rundir/01.raw_align/03.sort_align.sh.work/sort_align000/input.seed.053.sorted.ovl.bl', dbuf=False, fast=False, idxs='/GPFS/zhangli_lab_permanent/zengpeng/Pp/./01_rundir/02.cns_align//01.get_cns.input.idxs', max_cov_aln=130, max_lq_length=10000, min_cov_base=4, min_cov_seed=10, min_error_corrected_ratio=0.8, min_len_aln=500, min_len_seed=10000, out='cns.fasta', ovl='/GPFS/zhangli_lab_permanent/zengpeng/Pp/01_rundir/01.raw_align/03.sort_align.sh.work/sort_align000/input.seed.053.sorted.ovl', process=15, split=False)
[WARNING] 2019-11-26 10:01:20,541 Skip 494197 seeds in blacklist.
[INFO] 2019-11-26 10:01:20,638 Start a cns worker in 54776 from parent 54769
[INFO] 2019-11-26 10:01:20,638 Start a cns worker in 54778 from parent 54769
[INFO] 2019-11-26 10:01:20,639 Start a cns worker in 54777 from parent 54769
[INFO] 2019-11-26 10:01:20,640 Start a cns worker in 54780 from parent 54769
[INFO] 2019-11-26 10:01:20,640 Start a cns worker in 54779 from parent 54769
[INFO] 2019-11-26 10:01:20,640 Start a cns worker in 54781 from parent 54769
[INFO] 2019-11-26 10:01:20,641 Start a cns worker in 54782 from parent 54769
[INFO] 2019-11-26 10:01:20,641 Start a cns worker in 54783 from parent 54769
[INFO] 2019-11-26 10:01:20,643 Start a cns worker in 54785 from parent 54769
[INFO] 2019-11-26 10:01:20,643 Start a cns worker in 54784 from parent 54769
[INFO] 2019-11-26 10:01:20,644 Start a cns worker in 54786 from parent 54769
[INFO] 2019-11-26 10:01:20,644 Start a cns worker in 54787 from parent 54769
[INFO] 2019-11-26 10:01:20,645 Start a cns worker in 54788 from parent 54769
[INFO] 2019-11-26 10:01:20,645 Start a cns worker in 54789 from parent 54769
[INFO] 2019-11-26 10:01:20,646 Start a cns worker in 54790 from parent 54769
Failed read DB file [/GPFS/zhangli_lab_permanent/zengpeng/Pp/./01_rundir/01.raw_align/input.part.135.2bit] into buf, and disable module of reading DB files into buf and continue...
Failed read DB file [/GPFS/zhangli_lab_permanent/zengpeng/Pp/./01_rundir/01.raw_align/input.part.135.2bit] into buf, and disable module of reading DB files into buf and continue...
slurmstepd-c02b06n06: error: *** JOB 6145922 ON c02b06n06 CANCELLED AT 2019-11-26T10:04:08 ***
slurmstepd-c02b06n04: error: *** JOB 6145920 ON c02b06n04 CANCELLED AT 2019-11-26T10:04:08 ***
slurmstepd-c02b06n06: error: Detected 1 oom-kill event(s) in step 6145922.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.
slurmstepd-c02b06n04: error: Detected 1 oom-kill event(s) in step 6145920.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.
from nextdenovo.
Try to use the parameter: correction_options = -p 15 -dbuf
from nextdenovo.
it works, memory request < 3gb, but outputs very slowly.
from nextdenovo.
Use usetempdir
option or remove -dbuf
option, will speed up.
from nextdenovo.
Related Issues (20)
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- sort_align step erro HOT 1
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from nextdenovo.